The car is a 08 mazda 3 and everything is currently stock.
If this is enough money for a complete set up then I would like that but I am going for good quality and loud. Subs and Amp come before everything right now unless my budget can fit other speakers as well.
I just did the same car. If you are looking at upgrading more in the future I would start with deck, amp and subs. You can get a good deck for about $200. Sub and amps will cost you roughly $600 for good quality. Now if you are looking to have a nice looking system maybe consider buy both amps now as you may not be able to match them (appearance wise) when you want to by another one. I recommend having a box built rather than buying a premade one... I have yet to hear a premade box I like. Take a look at the Exile amps. You can get a S1000.1 and a S400.4 for $430 before tax. Personally? I would buy both amps, deck and subs which you should be able to do within $1000 and use the rest on the install. That way when you are ready to replace your other speakers you are ready to go.
Your stock deck does not have RCA out. You will get much better quality out of a new deck. I agree with it looking a little strange going with an aftermarket deck in that dash so I went with a double din deck. Cost is a little more but it fills the dash better. I went with 2 10" infinity subs and exile amps. Exile is a fairly new brand but they are the guys from Pheonix gold and the amps I got seem pretty good. I would go with a mono block amp for the subs and a 4 channel for the rest. take a look at my pics to get an idea if you want. I did my install myself and it is by no way anything special. just a basic install.